In eukaryotes, gene expression patterns are regulated in response to developmental and environmental cues. These changes in gene expression patterns are often the result of specific transcriptional regulators. In many cases, this change in gene expression must be stably maintained through many mitotic cell divisions even though the transcriptional regulator that effected the change in expression is only present transiently. The stable maintenance of a transcription state is performed by a set of nonspecific factors. These factors are important in regulating chromatin states and establishing a chromatin “memory” to effectively maintain the proper gene expression patterns. In Drosophila, the Polycomb group, PcG, genes are involved in nonspecific, long-term stabilization of transcriptional repression. Recently, homologs of some of the polycomb group genes have been shown to affect developmental gene regulation in other species.
There are at least thirteen PcG proteins in Drosophila. Mutations in any of the thirteen identified PcG genes can lead to lethality during early development (See, Simon, J., Current Opinion in Cell Biology, 7(3):376-85 (1995); Pirrotta, V., Curr. Opin. Gen. Dev., 7(2):249-58 (1997); Pirrotta, V., Cell, 93(3):333-6 (1998)). The cause of this lethality is the failure to maintain transcriptional repression of homeotic genes of the Antennopedia/bithorax complex. The expression pattern of these homeotic genes is controlled in the embryo by activators and repressors that define body segments. During gastrulation, these specific factors are no longer present and PcG protein complexes stabilize a silenced state at genes repressed by the specific factors. Importantly, PcG complexes silence different targets in different cell lineages. This indicates that PcG complexes are able to silence based on factors such as transcription state and not just on sequence. An antagonistic set of factors which maintain the active transcriptional state, the trithorax group, also exist in Drosophila. 
In addition to playing a role in developmentally regulated repression of gene expression, the PcG proteins are also involved in maintaining a silenced state at other loci. When high copy numbers (>3) of a white-Adh transgene are introduced into the Drosophila genome the level of white-Adh expression becomes reduced via cosuppression (Pal-Bhadra et al., Cell, 90:479-490 (1997)). In addition to reductions in the expression of the transgenes, the expression of the endogenous Adh gene is reduced as well. This cosuppression is relieved by mutations in polycomb (Pc) or polycomblike (pcl). The cosuppression is based on a homology sensing mechanism that leads to repression via PcG proteins (Pal-Bhadra et al., Cell, 99:35-46 (1999)). The PcG protein, enhancer of zeste, E(z), is required for trans-silencing of P-elements (Roche et al., Genetics, 149(4):1839-55 (1998)). Increased expression of E(z) or the human homolog (EZH2) results in enhancing position effect variegation (PEV) of a heterochromatin associated white locus (Laible et al., EMBO J., 16(11) 3219-32 (1997)). The EZH2 gene was also able to restore telomere mediated gene repression in S. cerevisiae (Laible et al., EMBO J., 16(11) 3219-32 (1997)). These studies suggest that the PcG proteins can play a role in epigenetic inactivation of gene expression distinct from the role of developmental regulation.
Many of the domains present in the PcG proteins that have been cloned are implicated in protein-protein interactions. The esc and E(z) proteins have been shown to interact with each other in a yeast two hybrid system and through in vitro binding assays (Jones et al., Cell Biol., 18(5):2825-34 (1998)). Homotypic and heterotypic interactions based on the SPM domain have been documented for Sex combs on midleg (Scm) and ph (Bornemann et al., Development, 122(5):1621-30 (1996); Peterson et al., Mol. Cell Biol., 17(11):6683-92 (1997)). The Xenopus Pc homolog, Xpc, forms complexes with itself and Bmi-1 (a psc homolog) (Reijnen et al., Mech. Dev., 53(1):35-46 (1995)). In other yeast two-hybrid screens, ph interacts with itself and with Psc, and Psc interacts with Pc (Pirotta, V., Curr. Opin. Gen. Dev., 7(2):249-58 (1997)). These results indicate the presence of a large complex formed by PcG proteins that is formed based on multiple protein-protein interactions among various PcG members.
Recent evidence suggests that PcG proteins actually form two distinct complexes. One complex contains E(z) and esc which have been found to directly interact (van Lohuizen et al., Mol. Cell Biol., 18(6):3572-9 (1998); Jones et al., Mol. Cell Biol., 18(5):2825-34 (1998), Sewalt et al., Mol. Cell Biol., 18(6):3586-95 (1998); Ng et al., Mol. Cell Biol., 20(9):3069-78 (2000)). The second complex is the PRC1 complex (which includes Pc/Ph/Scm/Psc).
Homologs from PcG proteins have been characterized in a number of species. Vertebrates appear to contain the most homologs of PcG proteins (Simon, Current Opinion in Cell Biology, 7(3):376-85 (1995)). Homologs of psc, Pc, ph, E(z) and esc have been cloned in mammals. The role of PcG proteins in mammals is believed to be very similar to the role in Drosophila. 
While many of the domains present in PcG proteins are found in yeast proteins, no PcG homologs are present in the S. cerevisiae genome. In C. elegans and Arabidopsis, homologs of two PcG proteins, E(z) and esc are found. A SET domain and a cys-rich region are found in E(z) (Carrington et al., Development, 122(12):4073-83 (1996); Jones et al., Genetics, 126(1):185-99 (1990); Jones, R S, et al., Mol. Cell. Biol., 13(10):6357-66 (1993)). The esc proteins contain a series of seven WD-40 repeats (Gutjahr et al., EMBO J., 14(17):4296-306 (1995); Simon et al., Mech. Devt., 53(2):197-208 (1995)).
The E(z) and esc homologs (maternal effect sterile-2 (mes-2) and maternal effect sterile-6 (mes-6)) from C. elegans were identified in a screen for maternal-effect mutations that result in sterile offspring (Holdeman et al., Development, 125(13):2457-67 (1998), Korf et al., Development, 125(13):2469-78 (1998)). The mes-2 and mes-6 genes are implicated as maternal genes required for germline immortality. Both mes-2 and mes-6 are localized to the nucleus of all embryonic cells and the nuclei of germline cells in larvae and adults. This localization is dependent upon each other and another protein, mes-3 (Holdeman et al., Development, 125(13):2457-67 (1998), Korf et al., Development, 125(13):2469-78 (1998)). Transgene arrays in the C. elegans genome are frequently silenced in germline cells (Kelly et al., Development, 125(13):2451-6 (1998)). Mutations in mes-2 and mes-6 completely alleviate silencing of transgenes in the germline cells (Kelly et al., Development, 125(13):2451-6 (1998). These results suggest that the PcG proteins of C. elegans, mes-2 and mes-6 are involved in transcriptional repression specifically in the germline cells. It is likely that mes-2 and mes-6 repress transcription of genes that would lead to a differentiated state.
Arabidopsis also contains homologs of E(z) and esc (Goodrich et al., Nature, 386(6620):44-51 (1997)), Grossniklaus et al., Science, 280(5362):446-50 (1998); Ohad et al., Plant Cell, 11(3):407-16 (1999)). Arabidopsis contains three E(z)-like genes, curly leaf (clf), Medea (Mea) and E(z)-likeA1 (EZA1) and one esc homolog, fertilization-independent endosperm (FIE1).
Clf mutants display curled leaves, altered maturation times and partial homeotic transformations of floral tissues (Goodrich et al., Nature, 386(6620):44-51 (1997)). Ectopic expression is also observed for the hometoic genes Agamous (AG) and Apetela3 (AP3). These genes are specifically expressed in floral tissues where clf mRNA is also present. This indicates that, similar to the Drosophila PcG proteins, the presence of CLF protein is not sufficient to repress AG and AP3 transcription but requires targeting factors (Goodrich et al., Nature, 386(6620):44-51 (1997)). The homeotic genes AG and AP3 are also ectopicly expressed in Arabidopsis plants with reduced methylation levels (Finnegan et al., Proc. Natl. Acad. Sci. USA, 93(16):8449-8454 (1996)).
Medea was identified in a screen for Arabidopsis gametophyte lethal mutations (Grossniklaus et al., Science, 280(5362):446-50 (1998); Chaudhury et al., Proc. Natl. Acad. Sci., USA, 94(8):4223-8 (1997); Luo et al., Proc. Natl. Acad. Sci. USA, 96(1):296-301 (1999)). A plant heterozygous for mea mutations will produce 50% aborted seeds that collapse and do not germinate. Subsequently it has been found that MEA exhibits an imprinted pattern of gene expression (Kinoshita et al., Plant Cell, 11(10):1945-52 (1999)); Vielle-Calzada et al., Genes Dev., 13(22):2971-82 (1999)). The maternal copy of Medea is expressed while the paternal copy is not. Medea mutants will allow endosperm development to occur in the absence of fertilization (Kiyosue et al., Proc. Natl. Acad. Sci. USA, 96(7):4186-91 (1999)). These results indicate that maternal expression of Medea is required to repress endosperm development. Due to the early lethality of Medea mutants, roles for Medea later in plant development have not been determined. A third E(z)-like gene, EZA1 is present in the Arabidopsis genome (Preuss, D., Plant Cell., 11(5):765-8 (1999)). Presently, the function of EZA1 is unknown.
Mutations in the Arabidopsis esc-like gene, FIE, have phenotypes similar to Medea. A female gametophyte with a FIE mutant allele will undergo replication of the central cell nucleus and endosperm development without a fertilization event (Ohad et al., Plant Cell, 11(3):407-16 (1999)). This indicates that FIE is critical in the repression of endosperm development. As with Medea, due to the early lethality of FIE mutants, the role of FIE in later developmental events has not been determined. The similar phenotypes of FIE and mea mutants suggests that these two genes may interact functionally like E(z) and esc homologs in other organisms.